Structurally colored residues

The position of rhodopsin in the membrane deduced from SDSL data is compatible with the topography of surface residues in the molecule. Figure 17B shows a space-filling model of the rhodopsin structure with residues color coded according to charge, polarity, and identity of tyrosines and tryptophans. It is clear that the demarcation between the charged and hydrophobic residues on the cytoplasmic surface defines... 

Fig. 5. The structures of unusual SH2 domain-containing proteins. (A) Stereo diagram of the N-terminal region of SAP in complex with a tyrosine phosphorylated peptide from SLAM. Color-coding of secondary structures and residues is as in Fig. 2. Note that the SAP SH2 domain makes extensive contacts with the residues of the peptide N-terminal region to the pTyr, an unusual feature for SH2 domains. (B) Stereo diagram...

Figure 4.7 Two of the enzymatic activities involved in the biosynthesis of tryptophan in E. coli, phosphoribosyl anthranilate (PRA) isomerase and indoleglycerol phosphate (IGP) synthase, are performed by two separate domains in the polypeptide chain of a bifunctional enzyme. Both these domains are a/p-barrel structures, oriented such that their active sites are on opposite sides of the molecule. The two catalytic reactions are therefore independent of each other. The diagram shows the IGP-synthase domain (residues 48-254) with dark colors and the PRA-isomerase domain with light colors. The a helices are sequentially labeled a-h in both barrel domains. Residue 255 (arrow) is the first residue of the second domain. (Adapted from J.P. Priestle et al., Proc.

Figure S.28 Schematic diagrams of the two-sheet P helix. Three complete coils of the helix are shown in (a). The two parallel P sheets ate colored gieen and red, the loop regions that connect the P strands ate yellow, (b) Each stmctuial unit Is composed of 18 residues forming a P-loop-P-loop structure. Each loop region contains six residues of sequence Gly-Gly-X-Gly-X-Asp where X is any residue. Calcium Ions are bound to both loop regions. (Adapted from F. Jumak et al., Ciirr. Opin. Struct. Biol. 4 802-806, 1994.)...

Figure 8.3 The DNA-binding protein Cro from bacteriophage lambda contains 66 amino acid residues that fold into three a helices and three P strands, (a) A plot of the Ca positions of the first 62 residues of the polypeptide chain. The four C-terminal residues are not visible in the electron density map. (b) A schematic diagram of the subunit structure. a helices 2 and 3 that form the helix-turn-helix motif ate colored blue and red, respectively. The view is different from that in (a), [(a) Adapted from W.F. Anderson et al., Nature 290 754-758, 1981. (b) Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.]...

Figure 9.17 Schematic diagram illustrating the tetrameric stmcture of the pS3 oligomerization domain. The four subunits have different colors. Each subunit has a simple structure comprising a p strand and an a helix joined by a one-residue turn. The tetramer is built up from a pair of dimers (yellow-blue and red-green). Within each dimer the p strands form a two-stranded antiparallel p sheet which provides most of the subunit interactions. The two dimers are held together by interactions between the four a helices, which are packed in a different way from a four-helix bundle. (Adapted from P.D. Jeffrey et al.. Science 267 1498-1502, 1995.)...

Figure 10.5 Comparison of the sequence-specific binding to DNA of six different zinc fingers. Residues in the N-terminus of the a helix in the finger regions are numbered 1 to 6. The residue immediately preceding the a helix is numbered -1. Amino acid residues and nucleotides that make sequence-specific contacts are colored. In spite of the structural similarities between the zinc fingers and their overall mode of binding, there is no simple rule that governs which bases the fingers contact.

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Illuvial accumulation of organic matter Residual accumulation of sesquioxides Illuvial accumulation of sesquioxides Accumulation of clay Development of color or structure... 

Fig. 2 Chemical shift perturbation and chemical shift mapping, (a) Portions of the [15N, 1H]-HSQC spectra of Bcf-xL recorded in absence (black) and in presence of each of the four molecules (in colors). Resonance assignments for amino acid residues that exhibit large shifts are reported, (b) Structure of Bc1-Xl in complex with the BH3 peptide from Bak (PDB code 1BXL) showing the chemical shift changes in Bcl-xL upon ligand binding (blue, large shits yellow, no shifts the Bak peptide is reported in cyan). Adapted from [48]...

Fig. 2.5. Interactions of chemokines with heparin disaccharides. (A to C) Monomeric forms of chemokines are displayed as cartoons with residues found to interact with heparin colored red. (A) Monomer of crystal structure of CCL5 (RANTES) with heparin disaccharide I-S bound (red). (B) CXCL4 (PF4) with low-molecular-weight heparin (MW <9000d). (C) CXCL8 with heparin disaccharide I-S. (D) CXCL12 (SDF-la) with heparin disaccharide I-S. (E) CCL2, human IP-10, with conserved residues from murine IP-10 highlighted.

Figure 7-2. Properties of CAII active site in the COHH state (zinc-bound hydroxide and protonated His 64). (a) Superposition of a few key residues from two stochastic boundary SCC-DFTB/MM simulations with the X-ray structure [87] (colored based on atom-types) the two sets of simulations did not have any cut-off for the electrostatic interactions between SCC-DFTB and MM atoms but used different treatments for the electrostatic interactions among MM atoms group-based extended electrostatics (in yellow) and atom-based force-shift cut-off (in green). Extended electrostatics simulations sampled configurations with the protonated His 64 too close to the zinc moiety while force-shift simulations consistently sampled the out configuration of His 64 in multiple trajectories, (b) Statistics for productive water-bridges (only from two and four shown here) between the zinc bound water and His 64 with different electrostatics protocols...

A model of a Pn helix formed by alanine side chains is illustrated for reference in Figure 13B (see color insert), while Figure 13A illustrates the common occurrence of the Pn backbone conformation among residues outside regions of regular secondary structure (Kleywegt and Jones, 1996 Serrano, 1995 Stapley and Creamer, 1999) in protein structures from the Protein Data Bank. 

A) general domain structure and position of the residues, (B) wild type, (C) mutant showing interaction of lie164 with Ser165 (see color plates, p. XXXII). 

Type 61b of the intensely colored quinocyclopropenes is represented by the di-cyanomethylene species 115 and 118 of p- and o-quinonoid structure. In addition to the systems 115,119, and 122 reported by Gompper1001 a series of o- and p-quino-cyclopropenes in the benzene, naphthalene, anthracene, phenanthrene, and fluorene series (718-125) were prepared75) carrying the bis-(p-anisyl)-cyclopropenyl residue, which brings about a better stabilization of the cyclopropenium moiety101 ... 

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